Hi Freesurfers,
Does anyone know if it is possible to manually set the brain centroid during the EM Registration step of the recon-all pipeline. I am using a non-default atlas, and have discovered that many of my difficulties have resulted from the brain centroid being incorrectly assigned to a region of black space. Thank you for the help!
Best,
MP
As a quick update to this problem, it looks like the wm_mean and gm_mean are reasonable during the #SkullLTA and #SkullStripping steps. However, wm mean = 0 and gm mean = 0 for the #CA_normalize and #EM_registration steps.
Could this have anything to do with using a manual talairach alignment in previous steps? I did include the -nogcareg flag with the recon-all command.
On Mon, May 12, 2014 at 4:36 PM, Mark Plantz < markplantz2016@u.northwestern.edu> wrote:
Hi Freesurfers,
Does anyone know if it is possible to manually set the brain centroid during the EM Registration step of the recon-all pipeline. I am using a non-default atlas, and have discovered that many of my difficulties have resulted from the brain centroid being incorrectly assigned to a region of black space. Thank you for the help!
Best,
MP
Hi Mark
did you create your own .gca file? If so, why? Does it happen for all your subjects? Bruce
On Mon, 12 May 2014, Mark Plantz wrote:
As a quick update to this problem, it looks like the wm_mean and gm_mean are reasonable during the #SkullLTA and #SkullStripping steps. However, wm mean = 0 and gm mean = 0 for the #CA_normalize and #EM_registration steps. Could this have anything to do with using a manual talairach alignment in previous steps? I did include the -nogcareg flag with the recon-all command.
On Mon, May 12, 2014 at 4:36 PM, Mark Plantz markplantz2016@u.northwestern.edu wrote: Hi Freesurfers, Does anyone know if it is possible to manually set the brain centroid during the EM Registration step of the recon-all pipeline. I am using a non-default atlas, and have discovered that many of my difficulties have resulted from the brain centroid being incorrectly assigned to a region of black space. Thank you for the help!
Best,
MP
Yes, I created my own atlas for use with 1-2 year olds. It seems to be happening for all of the subjects. I am wondering if changing the recon-all code to load the manual talairach.lta file for the EM_registration and CA_normalization would possibly fix the problem. It seems strange that the wm/gm means were OK for skull stripping, but then suddenly null for the other steps.
On Mon, May 12, 2014 at 7:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Mark
did you create your own .gca file? If so, why? Does it happen for all your subjects? Bruce
On Mon, 12 May 2014, Mark Plantz wrote:
As a quick update to this problem, it looks like the wm_mean and gm_mean
are reasonable during the #SkullLTA and #SkullStripping steps. However, wm mean = 0 and gm mean = 0 for the #CA_normalize and #EM_registration steps. Could this have anything to do with using a manual talairach alignment in previous steps? I did include the -nogcareg flag with the recon-all command.
On Mon, May 12, 2014 at 4:36 PM, Mark Plantz <markplantz2016@u. northwestern.edu> wrote: Hi Freesurfers, Does anyone know if it is possible to manually set the brain centroid during the EM Registration step of the recon-all pipeline. I am using a non-default atlas, and have discovered that many of my difficulties have resulted from the brain centroid being incorrectly assigned to a region of black space. Thank you for the help!
Best,
MP
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Hi Mark
if you upload a subject that failed and the gca I'll take a look Bruce On Mon, 12 May 2014, Mark Plantz wrote:
Yes, I created my own atlas for use with 1-2 year olds. It seems to be happening for all of the subjects. I am wondering if changing the recon-all code to load the manual talairach.lta file for the EM_registration and CA_normalization would possibly fix the problem. It seems strange that the wm/gm means were OK for skull stripping, but then suddenly null for the other steps.
On Mon, May 12, 2014 at 7:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Mark
did you create your own .gca file? If so, why? Does it happen for all your subjects? Bruce On Mon, 12 May 2014, Mark Plantz wrote: As a quick update to this problem, it looks like the wm_mean and gm_mean are reasonable during the #SkullLTA and #SkullStripping steps. However, wm mean = 0 and gm mean = 0 for the #CA_normalize and #EM_registration steps. Could this have anything to do with using a manual talairach alignment in previous steps? I did include the -nogcareg flag with the recon-all command. On Mon, May 12, 2014 at 4:36 PM, Mark Plantz <markplantz2016@u.northwestern.edu> wrote: Hi Freesurfers, Does anyone know if it is possible to manually set the brain centroid during the EM Registration step of the recon-all pipeline. I am using a non-default atlas, and have discovered that many of my difficulties have resulted from the brain centroid being incorrectly assigned to a region of black space. Thank you for the help! Best, MP
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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